I'd need the system in my hands to be sure, but are these typical 5mm encapsulated LEDs with a bullet shape, dome on the front?
If so, that shape is focusing the LEDs. Simply sand them flat, and if you want a little more forward light, polish the flat, fronts. I cannot say if this will be too much stress on the PCB they are mounted on, another complimentary option then is to build a dam around the LED circuit board, flood in between them with clear epoxy (use a decorative type that does not yellow with UV exposure, not just regular hardware store adhesive type) which will not only fortify the LED array when you sand but also diffuse some light all by itself.
Would it be too much? I have no idea what you are trying to achieve. I don't want to see my system at all.. under a desk.